Detailed stratigraphic study, paleoenvironmental interpretation of tidal wetland facies based on macroflora and agglutinated foraminiferal assemblages, radiocarbon dating, and modern marsh accretion rates are used to reconstruct the late Holocene sea-level history of the Leipsic River valley. Transgressive valley-fill deposits of the Leipsic River valley consist of brown peat, olive-gray mud, and gray-brown muddy peat. These facies were deposited in brackish wetland environments, open-water subtidal environments, and modern salt-marsh environments, respectively.

In the early Holocene the Leipsic River was a tributary to a major fluvial system, possibly the paleo–Delaware River. The Holocene transgression reached the area about 5,000 yr BP, when fringing tidal wetlands began to develop in both valleys, depositing brown peat. Rapidly rising sea level flooded the valley of the Leipsic River by 3,000 BP, turning it into an open-water estuarine environment. After 3,000 yr BP, the rate of the sea-level rise decreased, resulting in wide expansion of brackish wetlands in the Leipsic River valley and along the Delaware Bay coast. Tidal creeks migrating on the marsh paleosurface were eroding brown peat and depositing mud units at different depths. The brackish conditions persisted in the area until about 1,000 yr BP. One thousand years ago a change in the environments occurred when modern salt marshes began to replace the brackish wetlands.

Sea level was approximately 12 m below modern MHW when the first emergent tidal wetlands were developed in the valley. By 4000 yr BP, rapidly rising sea level reached an elevation of 9 m below MHW. From 4000 to 2000 yr BP, sea level rose to an elevation of 3.5 m, and by 1000 yr BP it reached an elevation of about 3 m below the modern marsh surface.

Salt marshes developed in the valley during the last 100 years with a vertical marsh accretion rate of 0.29 cm/yr. Twenty years ago, the marsh vertical accretion rate increased up to 0.46 cm/yr. These rates are comparable to the average rate of sea-level rise of 0.33 cm/yr measured by the tide gauge at Breakwater Harbor, Delaware. Thus, the salt marshes at Bombay Hook National Wildlife Refuge are in a dynamic equilibrium with rising sea level.